IncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome

Abstract

Background: Recent studies have demonstrated the importance of long non-coding RNAs (IncRNAs) in chromatin remodeling, and in transcriptional and post-transcriptional regulation. However, only a few specific IncRNAs are well understood, whereas others are completely uncharacterized. To address this, there is a need for user-friendly platform to studying the putative regulatory functions of human IncRNAs. Description: IncRNAMap is an integrated and comprehensive database relating to exploration of the putative regulatory functions of human IncRNAs with two mechanisms of regulation, by encoding siRNAs and by acting as miRNA decoys. To investigate IncRNAs producing siRNAs that regulate protein-coding genes, IncRNAMap integrated small RNAs (sRNAs) that were supported by publicly available deep sequencing data from various sRNA libraries and constructed IncRNA-derived siRNA-target interactions. In addition, IncRNAMap demonstrated that IncRNAs can act as targets for miRNAs that would otherwise regulate protein-coding genes. Previously studies indicated that intergenic IncRNAs (lincRNAs) either positive or negative regulated neighboring genes, therefore, IncRNAMap surveyed neighboring genes within a 1 Mb distance from the genomic location of specific IncRNAs and provided the expression profiles of IncRNA and its neighboring genes. The gene expression profiles may supply the relationship between incRNA and its neighboring genes. Conclusions: lncRNAMap is a powerful user-friendly platform for the investigation of putative regulatory functions of human IncRNAs with producing siRNAs and acting as miRNA decoy. IncRNAMap is freely available on the web at http://IncRNAMap.mbc.nctu.edu.tw/., (C) 2014 Elsevier Ltd. All rights reserved.